During the past century, anthropogenic activities have altered the distribution of mercury (Hg) on the earth's surface. The impacts of such alterations to the natural cycle of Hg can be minimized through coordinated management, policy decisions, and legislative regulations. An ability to quantitatively measure environmental Hg loadings and spatiotemporal trends of their fate in the environment is critical for science-based decision making. Here, we outline a Hg monitoring program for temperate estuarine and marine ecosystems on the Atlantic Coast of North America. This framework follows a similar, previously developed plan for freshwater and terrestrial ecosystems in the United States. Methylmercury (MeHg) is the toxicologically relevant form of Hg, and its ability to bioaccumulate in organisms and biomagnify in food webs depends on numerous biological and physicochemical factors that affect its production, transport, and fate. Therefore, multiple indicators are needed to fully characterize potential changes of Hg loadings in the environment and MeHg